Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate WP_012384543.1 BIND_RS07890 acetolactate synthase large subunit
Query= curated2:O53554 (515 letters) >NCBI__GCF_000019845.1:WP_012384543.1 Length = 513 Score = 479 bits (1233), Expect = e-139 Identities = 266/515 (51%), Positives = 334/515 (64%), Gaps = 7/515 (1%) Query: 1 MNGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYAR 60 MNGA++L+ TLV G++VCFANPGTSEMHFV+ALD + +R +LTLFEGVATGAADGYAR Sbjct: 1 MNGAESLLRTLVASGIEVCFANPGTSEMHFVSALDRIEGIRPVLTLFEGVATGAADGYAR 60 Query: 61 IAGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAG 120 +A +PAA LLHLGPGL NGLANLHNAR+A+ PMV ++GDHAT H++++ PL S++ A+A Sbjct: 61 MAEKPAATLLHLGPGLANGLANLHNARKAQTPMVNIIGDHATTHQRFETPLTSNVAALAQ 120 Query: 121 TVSGWVRRTEAAADVGADAEAAIAASR-SGSQIATLILPADVCWSDGAHAAAGVPAQAAA 179 VS WV V ADA A+ A+R + QIA+LILPAD W AA+ +P A Sbjct: 121 PVSHWVATCRGPKTVAADAARAVQAARVAPGQIASLILPADTAWQPAERAASPLPVMGPA 180 Query: 180 APVD--VGPVAGVLRSGEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTCLERG 237 D + L G A +L+ G A RG GL AA RI ATGAR LC+TF +ERG Sbjct: 181 PVSDQAITQARDALLLGN-AALLLRGTALRGRGLRAAGRIAAATGARLLCDTFTPRIERG 239 Query: 238 AGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHVLAEP 297 AG VERL Y A L G + L+L G ++PV+FFAYP PS L P C+V V + P Sbjct: 240 AGRVHVERLPYRPAPTMACLQGTRTLILVGTQAPVAFFAYPDQPSALTPPDCDVLVFSHP 299 Query: 298 -GGAADALAALADEVAPGTVAPVAGASRPQLP-TGDLTSVSAADVVGALLPERAIVVDES 355 AA+ L LA+ + G AP++ P+LP G L S ++G LPE AI+ DES Sbjct: 300 HEDAAEGLEQLAEAIGAGDYAPISPCKPPELPIEGGLDPESVMRIIGHYLPEDAIISDES 359 Query: 356 NTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAMYTIS 415 T G L A HD L L GGAIG G+P AVGAA+A P R V+ L++DGSAMYT+ Sbjct: 360 LTSGFLPYPLLDTALPHDHLHLAGGAIGDGLPVAVGAAIACPGRKVIALQADGSAMYTLQ 419 Query: 416 GLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMDFVKIAE 475 LW+QARE LD+TT+IY N AY +L EL VGA + GP A L D+ PT+++VK+AE Sbjct: 420 SLWTQAREQLDITTIIYANRAYKVLFEELHSVGA-AKAGPHAFSLFDLHDPTLNWVKLAE 478 Query: 476 GMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVV 510 GMGV ARRV ALR+A GP LI+VV+ Sbjct: 479 GMGVEARRVEDTRNLTSALRSAITGRGPRLIEVVL 513 Lambda K H 0.318 0.134 0.402 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 609 Number of extensions: 28 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 515 Length of database: 513 Length adjustment: 35 Effective length of query: 480 Effective length of database: 478 Effective search space: 229440 Effective search space used: 229440 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory